ArticleJournal of physics. Condensed matter : an Institute of Physics journal2011
Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach.
Article in Journal of physics. Condensed matter : an Institute of Physics journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Phage-like packing structures with mean field sequence dependence.Journal of computational chemistry · 2017Article
- Communication: Origin of the contributions to DNA structure in phages.The Journal of chemical physics · 2013Article
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3 authors.
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Abstract
A coarse grained model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider the contribution of unpaired dangling ends. The parameters of the model differ when representing a double stranded DNA section or a single stranded DNA section. The thermodynamic effects of the possibility of different dangling end combinations were considered in the presence of different types of surfaces. Configurational sampling was achieved by the Metropolis Monte Carlo method. To gain a more complete picture of the free energy changes, an estimation of the conformational entropy was included. We find a strong thermodynamic effect for dangling mismatches due to sequence requirements when they are nearer the surface as opposed to being held away from the surface.
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